Search Results for "protein protein interaction"
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Showing 519 open source projects for "protein protein interaction"
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PFAAT is a Java-based multiple sequence alignment editor and viewer designed for protein family analysis. You can download PFAAT from http://pfaat.sourceforge.net/
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iCn3D
Web-based protein structure viewer and analysis tool
"I see in 3D" (iCn3D) Structure Viewer is not only a web-based 3D viewer, but also a structure analysis tool interactively or in the batch mode using NodeJS scripts based on the npm package icn3d. iCn3D synchronizes the display of 3D structure, 2D interaction, and 1D sequences and annotations. Users' custom displays can be saved in a short URL or a PNG image. The complete package of iCn3D including Three.js and jQuery is in the directory "dist" after you get the source code with the "Code... -
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Make-A-Video - Pytorch (wip)
Implementation of Make-A-Video, new SOTA text to video generator
Implementation of Make-A-Video, new SOTA text to video generator from Meta AI, in Pytorch. They combine pseudo-3d convolutions (axial convolutions) and temporal attention and show much better temporal fusion. The pseudo-3d convolutions isn't a new concept. It has been explored before in other contexts, say for protein contact prediction as "dimensional hybrid residual networks". The gist of the paper comes down to, take a SOTA text-to-image model (here they use DALL-E2, but the same learning... -
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MzDOCK - Multiple Ligand Docking Tool
MzDOCK is A Virtual Screening Tool For Drug Discovery Research
- Molecular Docking Virtual Screening Tool To Aid In Drug Discovery Research. - Developed with Synchronized functioning of Python and Batch scripts - Compatible on Windows - Accepted on Journal of Computational Chemistry - DOI: 10.1002/jcc.27390 -Integerated With Pymol-open-source for visualizing interaction (PSE file) generated from MzDOCK - Integrated with Molecule Drawing Tool - JSME Editor - If you are facing any issues or for queries . Contact us - kabeermuzammil614@gmail.com... -
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aramultiomics
A toolkit for studying protein-protein/nucleic acid interaction
araMultiOmics consisted of seven modules where each module was created based on existing databases and software for studying protein binding sites/open chromatin regions, DNA-TF bonding profile, etc -
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The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.
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CPAT
RNA coding potential assessment tool
Using RNA-seq, tens of thousands of novel transcripts and isoforms have been identified (Djebali, et al Nature, 2012 , Carbili et al, Gene & Development, 2011) The discovery of these hidden transcriptome rejuvenate the need of distinguishing coding and noncoding RNA. However, Most previous coding potential prediction methods heavily rely on alignment, either pairwise alignment to search for protein evidence or multiple alignments to calculate phylogenetic conservation score (such as CPC... -
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OmicsSuite
OmicsSuite: a suite for multi-omics analysis and visualization.
OmicsSuite (https://github.com/OmicsSuite/, https://omicssuite.github.io), original name BioSciTools, a desktop program developed based on Java 11, aims to make new exploration and contribution to the development of bioinformatics, and realize data analysis and visualization in the fields of sequence analysis, multimomics (transcriptomics, genomics, protein omics, metabonomics, single cell), microbiology, clinical, etc. The program inherits the excellent interactive components, perfect analysis... -
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XLibraryDisplay
A sequence analysis tool for protein engineering
XLibraryDisplay is an intuitive sequence analysis program optimized for protein engineering. It is ideal for all directed evolution platforms including phage, ribosome, and yeast display. Analysis can be quickly done on hundreds to thousands of sequences. Best suited for Sanger sequencing. Requirements: Microsoft Windows XP, 7, 8, or 10 and Excel 2007, 2010, 2013, or 2016 Described in Stafford et al JCIM 2014: http://pubs.acs.org/doi/abs/10.1021/ci500362s -
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Comet MS/MS search engine
Comet open source tandem mass spectrometry (MS/MS) search engine.
September 2021: the code repository has migrate to https://github.com/UWPR/Comet Comet is an open source tandem mass spectrometry (MS/MS) sequence database search engine. It identifies peptides by searching MS/MS spectra against sequences present in protein sequence databases. Comet currently exists as a simple Windows or Linux command line binary that only does MS/MS database search. Supported input formats are mzXML, mzML, ms2, and Thermo RAW files. Supported output formats are tab... -
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EvidentialGene
Evidence Directed Gene Construction for Eukaryotes
... and assembly software, combining all evidence for genes, from expressed sequences, genome assembly sequences, related species protein sequences, and any other, to annotate and score gene constructions. Over-produced constructions are classified by gene evidence for best qualities per "locus", including genome-aligned and gene-transcript aligned (genome-free) locus identification. All software developed for EvidentialGene is publicly available. See project wiki/blog for notes. -
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MOLS 2.0 is a free and open-source software package for peptide modeling and protein-ligand docking. Authors: Dr. D. Sam Paul, Dr. S. Nehru Viji, Dr. P. Arun Prasad, Dr. K. Vengadesan, Dr. N. Gautham. If you use MOLS 2.0 for publication, please cite - D. Sam Paul, N. Gautham, MOLS 2.0: software package for peptide modeling and protein–ligand docking, Journal of Molecular Modeling 22 (2016) 1–9. Publications related to MOLS 2.0: 1. Vengadesan, K. & Gautham, N. Enhanced sampling...
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genppi
GENPPI: standalone software for creating protein interaction networks
Our software GENPPI is efficient because, for example, it creates interaction networks from the central genome of 50 species/lineages of Corynebacterium, with an average size of 2200 genes, in less than 40 minutes, on a conventional computer. Our software is compelling because the interaction networks that it creates reflect evolutionary relationships between species and obtained in Average Nucleotide Identity (ANI) analyzes. Also, It allows the user to define how he intends to explore the PP... -
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AutoDockParser
A tool for efficient processing of Docking results
AutoDock Suit is one of the most popular software for performing Molecular Docking and Virtual Screening. This suit offers two programs AutoDock and AutoDock Vina. AutoDock provides its output as Docking Log Files (DLG files), while the latter outputs in pdbqt format. Post-processing of these results has long remained a manual job and hence various protocols and workflows are designed that are user-specific. Manual processing of these results for subsequent interaction analysis has remained... -
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APBSmem is a Java-based graphical user interface for Poisson-Boltzmann electrostatics calculations at the membrane. APBS version 1.2.0 or later is required.
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ExtAncSeqMEGA is a program to extract ancestral DNA sequences that have been calculated by MEGA. ExtAncSeqProt is a program to extract ancestral PROTEIN sequences that have been estimated by MEGA. See the ReadMe file for details and documentation
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NifFINDER
A preditor of Nif proteins
Tool developed in MATLAB to identify the set of proteins encoded by the nifs genes (which are called Nifs). Niffinder identifies up to 24 Nifs - For each Nif protein an Artificial Neural Network (ANN) was built. -
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PSSPT
PSSPT (Protein Secondary Structure Prediction Tool)
PSSPT (Protein Secondary Structure Prediction Tool) Please, visit our GitHub page for more detail. -
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MANTI
MANTI - Mastering Advanced N-Termini Interpretation
MANTI is a one-stop shop N-termini annotation & evaluation solution. MANTI was previously (un)known as muda.pl ahead of v3.7, the project was renamed to MANTI.pl with v3.7 on 2019-06-24. It congregates information from different MaxQuant or DiaNN/MSFragger output files into a master file suitable explicitly for protein neo-termini analyses. The central anchor for the data congregation is the modificationSpecificPeptides.txt or diann-output.pr_matrix.tsv file - additional data is inferred... -
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Finding DNA Repeats by RFRE
RFRE is a tool to find DNA repeats (tandem and short)
... Regular Expression Tool Regular Expression for Protein Motif Search and SSR sequence. https://sourceforge.net/projects/rfret/files/RFRE122019.exe/download https://www.preprints.org/manuscript/201910.0249/v1 https://sites.google.com/must.edu.eg/finding-dna-repeats/home ---------------------------------------------- *****Very important program must be downloaded before you run the EXE FILE OF RFRE***** 1-VB6 Runtime Plus 2.2.exe , https://sourceforge.net/projects/vb6extendedruntime/ -
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iem-configurator
Configurator for protein substitutes
This configurator helps you to calculate optimal dosage of protein substitutes. -
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comer2
COMER2, cross-platform software for protein remote homology search
The COMER method based on sequence profile-profile comparison is one of the most sensitive and accurate computational tools developed for protein alignment and homology search. COMER version 2.1 (COMER2) represents one of the fastest implementations of calculations for sensitive protein homology search. High COMER2 performance is achieved by harnessing the power of the Graphics processing unit (GPU). Hence, a GPU is expected to be installed on the system. The files include the compressed... -
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Shetti-Motif can be downloaded from the site (https://sites.google.com/site/haithamsobhy/software). Please, do not hesitate to contact Dr. Haitham Sobhy if you need help. Short linear motifs / domains (SLiM) facilitate the functions and interactions of the proteins. Finding functional motifs in protein sequences could predict the putative cellular roles or characteristics of hypothetical proteins. ShettiMotif, which is an interactive tool to (i) searches for motifs containing repeated...
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trilat-umn
Using FRET distances to trilaterate the location of a FRET acceptor
This software performs trilateration using an arbitrary number of donor sites and FRET distances with the aim to locate the position of a FRET acceptor in a protein structure. Our trilateration approach takes into account Gaussian distance distributions as fitted to the FLT-FRET measurement for each donor position. The normalized sum of the distance distributions from all of the donor sites to one acceptor is generated as a probability map describing the acceptor’s location. This volumetric map...